def cms(s, sel):
at = getAtomtypes()
if at is None:
msg().error(
"Atom-types information not available, calculating average.")
if s is None:
return None
s = Structure(s)
s.setCarthesian()
w = Vector(0.0, 0.0, 0.0)
M = 0.0
try:
for i, nx, ny, nz in sel:
if i < len(s) and i >= 0:
try:
m = float(s.info.getRecordForAtom(i).mass)
except:
m = float(
at.getRecordForElement(
s.info.getRecordForAtom(i).element).mass)
w = w + m * (s[i] + nx * s.basis[0] + ny * s.basis[1] +
nz * s.basis[2])
M = M + m
w = (1.0 / M) * w
return w
except:
msg().exception()
msg().error("CMS not aplicable, calculating an average.")
return average(s, sel)
def last(s, sel):
if s is None:
return None
s = Structure(s)
s.setCarthesian()
if len(sel):
i, nx, ny, nz = sel[-1]
if len(s) > i:
return s[i] + nx * s.basis[0] + ny * s.basis[1] + nz * s.basis[2]
return None
def readStructure(self, Id, cstructure=False):
s = Structure()
l = self.fetchone(
"""SELECT calc_id,scale,comment,a11,a12,a13,a21,a22,a23,a31,a32,a33,
species FROM #STRUCT WHERE id=%d""" % (Id))
(calc_id, scale, s.comment, s.basis[0][0], s.basis[0][1],
s.basis[0][2], s.basis[1][0], s.basis[1][1], s.basis[1][2],
s.basis[2][0], s.basis[2][1], s.basis[2][2], spec) = l
s.scaling = [scale]
s.setCartesian()
l = self.fetchall(
"SELECT specie,element,x,y,z FROM #STRUCTPOS WHERE structure_id=%d ORDER BY atomnumber"
% (Id))
for spec, element, x, y, z in l:
i = s.appendAtom(spec, Vector(x, y, z))
s.info.getRecordForAtom(i).element = str(element)
l = self.fetchall(
"SELECT x,y,z FROM #STRUCTCONSTRAINTS WHERE structure_id=%d ORDER BY atomnumber"
% (Id))
if len(l):
s.setSelective()
for i in range(len(l)):
s.selective[i] = [int(l[i][0]), int(l[i][1]), int(l[i][2])]
if cstructure:
s = p4vasp.cStructure.Structure(s)
return s
def average(s, sel):
if s is None:
return None
s = Structure(s)
s.setCarthesian()
w = Vector(0.0, 0.0, 0.0)
n = 0
for i, nx, ny, nz in sel:
if i < len(s) and i >= 0:
w = w + s[i] + nx * s.basis[0] + ny * s.basis[1] + nz * s.basis[2]
n = n + 1
w = (1.0 / float(n)) * w
return w
def storeStructure(self, s, step=None):
calc_id = self.calc_id
if calc_id is not None and step is not None:
for l in self.fetchall(
"SELECT id FROM #STRUCT WHERE calc_id=%d AND step=%d" %
(calc_id, step)):
removeStructure(db, l[0])
info = s.info
if len(s.scaling) != 1:
s.correctScaling()
cmd = "%s, %s," % (von(calc_id), von(step))
cmd += "%14.12f,'%s'," % (s.scaling[0], s.comment)
cmd += """%14.12f,%14.12f,%14.12f,
%14.12f,%14.12f,%14.12f,
%14.12f,%14.12f,%14.12f,%d""" % (
s.basis[0][0], s.basis[0][1], s.basis[0][2], s.basis[1][0],
s.basis[1][1], s.basis[1][2], s.basis[2][0], s.basis[2][1],
s.basis[2][2], s.types)
Id = self.insertRecord(
"#STRUCT", "id",
"calc_id, step, scale,comment,a11,a12,a13,a21,a22,a23,a31,a32,a33,species",
cmd)
if s.isSelective():
sel = s.selective
for i in range(len(sel)):
self.exe(
"""INSERT INTO #STRUCTCONSTRAINTS (structure_id,calc_id,atomnumber,x,y,z)
VALUES (%d,%s,%d,%d,%d,%d)""" %
(Id, von(calc_id), i, sel[i][0], sel[i][1], sel[i][2]))
sc = Structure()
sc.setStructure(s)
sc.setCartesian()
for i in range(len(s)):
si = s.speciesIndex(i)
self.exe(
"""INSERT INTO #STRUCTPOS (structure_id,calc_id,atomnumber,specie,element,x,y,z)
VALUES (%d,%s,%d,%d,'%s',%14.12f,%14.12f,%14.12f)""" %
(Id, von(calc_id), i, si, info[si].element, sc[i][0], sc[i][1],
sc[i][2]))
self.commit()
return Id
#!/usr/bin/env python
# this script extracts the atomic displacements from
# the DISP file generated by Phon,
# and creates POSCAR files for corresponding displacements
from p4vasp.SystemPM import *
from p4vasp.Structure import Structure
#run=XMLSystemPM('vasprun.xml')
#struct=run.FINAL_STRUCTURE
struct = Structure("POSCAR")
dispfile = open("DISP", 'r')
runfile = open("runhf", 'w')
runfile.write("#!/bin/bash \n")
runfile.write("VASP='vasp' \n\n")
disp = []
pos = []
pos.append(struct)
pos[len(pos) - 1].write('pos' + repr(len(pos) - 1))
for line in dispfile:
str = eval(line)
liststr = str.split()
listnum = []
for item in liststr:
listnum.append(eval(item))
def vectorEqual(x, y, eps):
"""check wether two vectors (hashable containers of numbers) are equal."""
if len(x) != len(y): return False
res = True
for (xi, yi) in zip(x, y):
res = res & isNearlyZero(xi - yi, eps)
# this could be made more efficient'
# since they are unequal as soon as a pair of components are not equal
return res
# name of distortion
name = "X3-_sym1"
# load a structure from existing POSCAR file:
struct = Structure("POSCAR_X3-")
print "Loaded POSCAR."
cellvolume = struct.getCellVolume()
print "Cell volume: ", cellvolume
# backup the original structure
#struct.write("POSCAR_X3-_ref", newformat=0)
# open output file:
outfile = open('frozen_phonon_' + name + '.dat', 'w')
# load the symmetry vector
try:
symfile = open("symmetryvector.in", 'r')
except:
IOError, "symmetryvector.in file not found"
def CalculateElasticConstant(straintype):
"""Calculate the elastic constant corresponding to straintype
using ab-initio energy calculation (VASP).
For a C11 deformation, one can use the deformation tensor:
[[1 0 0]
[0 0 0]
[0 0 0]]
For a C11-C12 deformation, one can use the deformation tensor:
[[1 0 0]
[0 -1 0]
[0 0 0]]
( 8 symmetry operators)
or:
[[1 0 0]
[0 1 0]
[0 0 -2]]
(16 symmetry operators)
For a C44 deformation, one can use the deformation tensor:
[[0 0 0]
[0 0 1]
[0 1 0]]
(4 symmetry operators)
or:
[[0 1 1]
[1 0 1]
[1 1 0]]
(12 symmetry operators)
All these tensors are now listed in the module CubicStandardStrainTensors.
"""
# load a structure from existing POSCAR file:
struct = Structure("POSCAR")
cellvolume = struct.getCellVolume()
# define a sequence of strain amplitudes:
strains=scipy.arange(-0.020, 0.022, 0.002).round(5)
# For a C11 deformation, one can use the deformation tensor:
# [[1 0 0]
# [0 0 0]
# [0 0 0]]
#
# For a C11-C12 deformation, one can use the deformation tensor:
# [[1 0 0]
# [0 -1 0]
# [0 0 0]]
# ( 8 symmetry operators)
# or:
# [[1 0 0]
# [0 1 0]
# [0 0 -2]]
# (16 symmetry operators)
#
# For a C44 deformation, one can use the deformation tensor:
# [[0 0 0]
# [0 0 1]
# [0 1 0]]
# (4 symmetry operators)
# or:
# [[0 1 1]
# [1 0 1]
# [1 1 0]]
# (12 symmetry operators)
# all these tensors are now listed in the module CubicStandardStrainTensors
import CubicStandardStrainTensors as cubic
# straintype = 'C44_2'
tens = cubic.__dict__[straintype]
# tens = cubic.__dict__['C44_2']
# tensor = p4mat.Matrix([[1.0, 0.0, 0.0],[0.0, 0.0, 0.0],[0.0, 0.0, 0.0]])
tensor = p4mat.Matrix( tens.tolist() )
# cmd='rsh -. n00 mpirun -np 8 vasp'
cmd = 'mr vasp'
# Generate the strained POSCAR files
GenStrainPoscar(struct, tensor, strains, straintype)
# Execute the VASP command on the sequence of POSCAR files
CalcStrains(strains, straintype, cmd)
print "Finished calculating strains."
# Collect the energies from the output vasprun.xml files.
runs=[]
energies=[]
forces=[]
for x in strains:
runs.append(XMLSystemPM('vasprun_'+straintype+'_'+repr(x)+'.xml'))
energies.append(runs[-1].FREE_ENERGY)
pass
for i in range(len(runs)):
print runs[i].FINAL_STRUCTURE.getCellVolume()
# for i in range(len(runs)):
# forces.append(runs[i].FORCES_SEQUENCE)
pass
evec=np.array(energies)
data=scipy.zeros((len(evec),2), dtype='f')
# We build the data to outfile to file, which is used later for fitting
# the strains are saved to file in Angstroems, not fractional coordinates
# if the structure read from the POSCAR file is "direct", we need to apply scaling:
# if struct.isDirect():
# scaling = struct.scaling[0]
# data[:,0] = strains * scaling
# else the strains are already in units of length (assumed Angstroems):
# elif struct.isCartesian():
# data[:,0] = strains
data[:,0] = strains
data[:,1] = evec
datafile=open(straintype+"_data.dat", 'w')
scipy.io.write_array(datafile, data)
datafile.close()
elastConst = FitCubicStrain(straintype+"_data.dat", straintype, cellvolume)
print straintype, ": ", elastConst
print straintype, " (GPa) : ", elastConst*160.22
print "Finished all."
pass # End of CalculateElasticConstant
def updateCoord(self):
s=self.getStructure()
if s is not None:
s=Structure(s)
s.setCarthesian()
sel=self.sel
if len(sel)>1:
try:
i,nx,ny,nz=sel[0]
v1=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
i,nx,ny,nz=sel[1]
v2=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
l=(v1-v2).length()
self.l1_entry.set_text("%14.8f"%l)
except:
self.l1_entry.set_text("")
else:
self.l1_entry.set_text("")
if len(sel)>2:
try:
i,nx,ny,nz=sel[0]
a=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
i,nx,ny,nz=sel[1]
b=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
i,nx,ny,nz=sel[2]
c=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
l=(b-c).length()
self.l2_entry.set_text("%14.8f"%l)
angle=(a-b).angle(c-b)*180.0/pi
self.a2_entry.set_text("%+7.4f"%angle)
except:
msg().exception()
self.l2_entry.set_text("")
self.a2_entry.set_text("")
else:
self.l2_entry.set_text("")
self.a2_entry.set_text("")
if len(sel)>3:
try:
i,nx,ny,nz=sel[0]
a=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
i,nx,ny,nz=sel[1]
b=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
i,nx,ny,nz=sel[2]
c=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
i,nx,ny,nz=sel[3]
d=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
l=(d-c).length()
self.l3_entry.set_text("%14.8f"%l)
angle=(b-c).angle(d-c)*180.0/pi
self.a3_entry.set_text("%+7.4f"%angle)
try:
dihedral=(c-b).cross(a-b).angle((b-c).cross(d-c))*180.0/pi
self.d3_entry.set_text("%+7.4f"%dihedral)
except:
self.d3_entry.set_text("")
except:
msg().exception()
self.l3_entry.set_text("")
self.a3_entry.set_text("")
self.d3_entry.set_text("")
else:
self.l3_entry.set_text("")
self.a3_entry.set_text("")
self.d3_entry.set_text("")
def vectorEqual(x,y, eps):
"""check wether two vectors (hashable containers of numbers) are equal."""
if len(x) != len(y): return False
res = True
for (xi, yi) in zip(x,y):
res = res & isNearlyZero(xi-yi, eps)
# this could be made more efficient'
# since they are unequal as soon as a pair of components are not equal
return res
# name of distortion
name = "X3-_sym1"
# load a structure from existing POSCAR file:
struct = Structure("POSCAR_X3-")
print "Loaded POSCAR."
cellvolume = struct.getCellVolume()
print "Cell volume: ", cellvolume
# backup the original structure
#struct.write("POSCAR_X3-_ref", newformat=0)
# open output file:
outfile = open('frozen_phonon_'+name+'.dat', 'w')
# load the symmetry vector
try:
symfile = open("symmetryvector.in", 'r')
except: IOError, "symmetryvector.in file not found"
from p4vasp.db import *
from p4vasp.Structure import Structure
from sys import stdout
db = getDatabase()[0]
db.connect()
db.addUser()
path = "XDATCAR"
s = Structure(path)
s.write(stdout)
f = open(path)
for i in range(8):
f.readline() #Skip header
db.addRecord(keywords="MD,XDATCAR", name=s.comment)
step = 0
while 1:
for i in range(len(s)):
s[i] = map(float, f.readline().split())
step += 1
#s.write(stdout)
db.storeStructure(s, step)
if f.readline().strip() != "":
break